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The Evil Genius is the player's avatar chosen from one of three evil characters to represent your quest for world domination. He or she possesses vast wealth and resources, and will use them to finance a global-spanning criminal organization that answers only to him or her to carry out your evil plans, referred to simply as "the evil organization" in the game.

Your mastermind does no work themselves, but relies on minions to build rooms, operate your equipment, research new technology, and deal with enemy agents. He or she also sends minions out into the world in order to steal money and raise your notoriety by planning and performing devious crimes, like assassination, sabotage, persuasion, taking over businesses and nations, causing major disasters, power broking, stealing treasures and equipment, capturing hostages that hold useful information, etc.

To further your evil goals, he or she also schemes to consolidate power over the criminal underworld, raise assets in money and loot to purchase a bigger island, use puppet diplomats to influence the world alliances, find the weaknesses of super agents that will allow you to eliminate them, and gather the information and objects needed to build the ultimate doomsday device you will use to dominate the entire world.

There are three Evil Geniuses to choose as your avatar for the game, with each one having special abilities and influence on your operation.

Maximilian: A wealthy industrialist who has the ambition to control the world through advanced scientific research and technological supremacy.

Alexis: A beautiful heiress to a media empire with a beloved presence the world over, allowing her to command the utmost respect and loyalty from those who serve under her.

Shen Yu: The clandestine super-criminal with a global network of conspirators that gives him hidden influence over the governments of the world.

These characters are essential to the completion of their plan for world domination, and must be kept safe at all costs. If they get hurt, they can heal through the Inner Sanctum, but if they are killed, the game automatically ends. After which, you are shown a short, but interesting cutscene in which your Evil Genius is taken to a morgue, but is revealed to be a robot double with an explosive set to blow up in three seconds when his or her fake head opens, giving the player another chance to start over.

Aura of Influence: All three Evil Geniuses radiate an aura from their person that restores the attention and loyalty of minions nearby. Alexis has the largest aura, but the slowest restoration rate. Shen Yu has the smallest aura, but the fastest restoration rate. Both Maximilian's aura size and regeneration rate are about average.

Executions: They have the ability to execute their minions to rapidly restore all five stats to all minions who are nearby watching the execution. The amount by which the stats of the nearby minions get boosted is however different with every Evil Genius: Maximilian boosts minion stats by 5, Shen Yu boosts them by 7, and Alexis by 10.

Taunting: Also, if you select your Evil Genius and select a cell with an agent inside, you will see a Ha Ha icon. Select this and your character will walk over and start gloating over the prisoner. This increases notoriety by 1.

Interrogation: If your Evil Genius is standing nearby while an enemy agent is being tortured on any device, you will gain up to five notoriety points, depending on the agent being interrogated. If a Super Agent is being destroyed, your Evil Genius will make his/her way over to the interrogation scene automatically, and stand laughing uproariously while the Super Agent is gotten rid of once and for all.